[English] 日本語
Yorodumi
- PDB-3lvk: Crystal Structure of E.coli IscS-TusA complex (form 2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lvk
TitleCrystal Structure of E.coli IscS-TusA complex (form 2)
Components
  • Cysteine desulfurase
  • Sulfurtransferase tusA
KeywordsTRANSFERASE / protein-protein complex / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / tRNA thiolation / sulfur transfer
Function / homology
Function and homology information


tRNA wobble position uridine thiolation / L-cysteine desulfurase complex / sulfur carrier activity / cysteine desulfurase / cysteine desulfurase activity / [2Fe-2S] cluster assembly / tRNA processing / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / metal ion binding / cytoplasm
Similarity search - Function
Sulfur carrier protein TusA / TusA-like domain / Uncharacterized protein family UPF0033 signature. / TusA-like domain / Sulfurtransferase TusA / TusA-like domain superfamily / Cysteine desulfurase IscS / Cysteine desulfurase / Translation Initiation Factor IF3 / Aminotransferase class-V, pyridoxal-phosphate binding site ...Sulfur carrier protein TusA / TusA-like domain / Uncharacterized protein family UPF0033 signature. / TusA-like domain / Sulfurtransferase TusA / TusA-like domain superfamily / Cysteine desulfurase IscS / Cysteine desulfurase / Translation Initiation Factor IF3 / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Cysteine desulfurase IscS / Sulfur carrier protein TusA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.442 Å
AuthorsShi, R. / Proteau, A. / Matte, A. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Plos Biol. / Year: 2010
Title: Structural basis for Fe-S cluster assembly and tRNA thiolation mediated by IscS protein-protein interactions.
Authors: Shi, R. / Proteau, A. / Villarroya, M. / Moukadiri, I. / Zhang, L. / Trempe, J.F. / Matte, A. / Armengod, M.E. / Cygler, M.
History
DepositionFeb 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cysteine desulfurase
B: Sulfurtransferase tusA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6933
Polymers56,4452
Non-polymers2471
Water82946
1
A: Cysteine desulfurase
B: Sulfurtransferase tusA
hetero molecules

A: Cysteine desulfurase
B: Sulfurtransferase tusA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,3856
Polymers112,8914
Non-polymers4942
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area8830 Å2
ΔGint-53 kcal/mol
Surface area34690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.893, 131.407, 106.411
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Cysteine desulfurase


Mass: 47326.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 EDL933 / Gene: iscS / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A6B9, cysteine desulfurase
#2: Protein Sulfurtransferase tusA


Mass: 9118.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 EDL933 / Gene: tusA / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A892, Transferases; Transferring sulfur-containing groups; Sulfurtransferases
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 0.12M Magnisum Formate, vapor diffusion, sitting drop, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.442→50 Å / Num. obs: 17507 / % possible obs: 91.3 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.077 / Χ2: 0.999 / Net I/σ(I): 15.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.442-2.545.20.38510920.97658.3
2.54-2.645.70.34813651.00272.6
2.64-2.766.40.33816190.99785.3
2.76-2.97.50.318581.00397.6
2.9-3.098.50.2518920.991100
3.09-3.328.70.16219191.003100
3.32-3.668.60.10119041.003100
3.66-4.198.60.07519241.002100
4.19-5.288.50.05519470.999100
5.28-507.90.03919871.00297.4

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6_289refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P3W and 1DCJ

1p3w

1dcj


Resolution: 2.442→41.348 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.32 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 883 5.06 %
Rwork0.207 --
obs0.209 17452 90.25 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.097 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso max: 193.04 Å2 / Biso mean: 82.174 Å2 / Biso min: 33.12 Å2
Baniso -1Baniso -2Baniso -3
1--12.637 Å20 Å2-0 Å2
2--27.952 Å20 Å2
3----15.314 Å2
Refinement stepCycle: LAST / Resolution: 2.442→41.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3619 0 15 46 3680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073700
X-RAY DIFFRACTIONf_angle_d1.014997
X-RAY DIFFRACTIONf_chiral_restr0.073556
X-RAY DIFFRACTIONf_plane_restr0.004650
X-RAY DIFFRACTIONf_dihedral_angle_d19.6151385
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.442-2.5950.3241200.2681778189860
2.595-2.7960.3261430.2662525266884
2.796-3.0770.3141540.2723002315699
3.077-3.5220.2641680.24330423210100
3.522-4.4360.2451510.18430813232100
4.436-41.3540.191470.1723141328898
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8818-0.26161.72252.0951-0.04294.3631-0.47490.62860.235-0.0896-0.0809-0.0859-0.53651.07110.00020.4254-0.1686-0.06450.5410.15360.453412.0429-25.173321.4371
21.92140.02430.70892.29910.57771.5427-0.67070.09190.41930.08190.15230.2136-0.70050.6823-0.00020.8951-0.282-0.29190.74410.18750.656226.5029-14.896345.427
30.3859-0.2161-0.29640.32810.40660.4732-0.52881.53120.2198-0.2692-0.03070.0268-1.5240.5516-0.00021.0334-0.2643-0.34791.50340.31120.80762.3603-16.8735-5.6226
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 12:263)A12 - 263
2X-RAY DIFFRACTION2(chain A and resid 1:11) or (chain A and resid 264:392)A1 - 11
3X-RAY DIFFRACTION2(chain A and resid 1:11) or (chain A and resid 264:392)A264 - 392
4X-RAY DIFFRACTION3(chain B and resid 4:79)B4 - 79

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more